Ecological aspects of the relatively diverse fish assemblages found in the terminal reaches of streams in Hawai'i are largely unknown. This study described patterns of microhabitat use in an assemblage of native and introduced stream fishes living in the terminal reach of Wailoa Stream on the island of Hawai'i. Multivariate analyses of data collected through underwater visual surveys indicated that differences in microhabitat use were an important factor in structure of this assemblage. In riffle habitats, native fishes selected distinct microhabitats based on water velocity, substrate size, and position in the water column. In run habitats, a benthic guild (native gobies) and a water-column guild (introduced poeciliids and the endemic Kuhlia xenura) were identified. Strong differences in three-dimensional microhabitat use patterns appear to allow native gobioids to resist being displaced by introduced poeciliids in Wailoa Stream. However, high overlap in the microhabitat use patterns of juvenile K. xenura and introduced Poecilia mexicana and Xiphophorus helleri is cause for concern.